atavide

Version 1

atavide is a complete workflow for metagenomics data analysis, including QC/QA, optional host removal, assembly and cross-assembly, and individual read based annotations. We have also built in some advanced analytics including tools to assign annotations from reads to contigs, and to generate metagenome-assembled genomes in several different ways, giving you the power to explore your data!

atavide is 100% snakemake and conda, so you only need to install the snakemake workflow, and then everything else will be installed with conda.

Steps:

1. QC/QA with prinseq++
2. optional host removal using bowtie2 and samtools, as described previously. To enable this, you need to provide a path to the host db and a host db.

Metagenome assembly

1. pairwise assembly of each sample using megahit
2. extraction of all reads that do not assemble using samtools flags
3. assembly of all unassembled reads using megahit
4. compilation of all contigs into a single unified set using Flye
5. comparison of reads -> contigs to generate coverage

MAG creation

1. metabat
2. concoct
3. Pairwise comparisons using turbocor followed by clustering

Read-based annotations

1. Kraken2
2. singlem
3. SUPER-focus
4. FOCUS

Want something else added to the suite? File an issue on github and we'll add it ASAP!

Installation

You will need to install

1. The NCBI taxonomy database somewhere
2. The superfocus databases somewhere, and set the SUPERFOCUS_DB environmental variable

Everything else should install automatically.